title: Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori.
abstract: The establishment of a complete genomic sequence of silkworm, the model species of Lepidoptera, laid a foundation for its functional genomics. A more complete annotation of the genome will benefit functional and comparative studies and accelerate extensive industrial applications for this insect. To realize these goals, we embarked upon a large-scale full-length cDNA collection from 21 full-length cDNA libraries derived from 14 tissues of the domesticated silkworm and performed full sequencing by primer walking for 11,104 full-length cDNAs. The large average intron size was 1904 bp, resulting from a high accumulation of transposons. Using gene models predicted by GLEAN and published mRNAs, we identified 16,823 gene loci on the silkworm genome assembly. Orthology analysis of 153 species, including 11 insects, revealed that among three Lepidoptera including Monarch and Heliconius butterflies, the 403 largest silkworm-specific genes were composed mainly of protective immunity, hormone-related, and characteristic structural proteins. Analysis of testis-/ovary-specific genes revealed distinctive features of sexual dimorphism, including depletion of ovary-specific genes on the Z chromosome in contrast to an enrichment of testis-specific genes. More than 40% of genes expressed in specific tissues mapped in tissue-specific chromosomal clusters. The newly obtained FL-cDNA sequences enabled us to annotate the genome of this lepidopteran model insect more accurately, enhancing genomic and functional studies of Lepidoptera and comparative analyses with other insect orders, and yielding new insights into the evolution and organization of lepidopteran-specific genes.
authors.affiliation: National Institute of Agrobiological Sciences, Tsukuba 305-8634, Japan.
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Suetsugu
authors.forename: Ryo
authors.initials: R
authors.lastname: Futahashi
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kanamori
authors.forename: Keiko
authors.initials: K
authors.lastname: Kadono-Okuda
authors.forename: Shun-ichi
authors.initials: S
authors.lastname: Sasanuma
authors.forename: Junko
authors.initials: J
authors.lastname: Narukawa
authors.forename: Masahiro
authors.initials: M
authors.lastname: Ajimura
authors.forename: Akiya
authors.initials: A
authors.lastname: Jouraku
authors.forename: Nobukazu
authors.initials: N
authors.lastname: Namiki
authors.forename: Michihiko
authors.initials: M
authors.lastname: Shimomura
authors.forename: Hideki
authors.initials: H
authors.lastname: Sezutsu
authors.forename: Mizuko
authors.initials: M
authors.lastname: Osanai-Futahashi
authors.forename: Masataka G
authors.initials: MG
authors.lastname: Suzuki
authors.forename: Takaaki
authors.initials: T
authors.lastname: Daimon
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Shinoda
authors.forename: Kiyoko
authors.initials: K
authors.lastname: Taniai
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Asaoka
authors.forename: Ryusuke
authors.initials: R
authors.lastname: Niwa
authors.forename: Shinpei
authors.initials: S
authors.lastname: Kawaoka
authors.forename: Susumu
authors.initials: S
authors.lastname: Katsuma
authors.forename: Toshiki
authors.initials: T
authors.lastname: Tamura
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Noda
authors.forename: Masahiro
authors.initials: M
authors.lastname: Kasahara
authors.forename: Sumio
authors.initials: S
authors.lastname: Sugano
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Haruhiko
authors.initials: H
authors.lastname: Fujiwara
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kataoka
authors.forename: Kallare P
authors.initials: KP
authors.lastname: Arunkumar
authors.forename: Archana
authors.initials: A
authors.lastname: Tomar
authors.forename: Javaregowda
authors.initials: J
authors.lastname: Nagaraju
authors.forename: Marian R
authors.initials: MR
authors.lastname: Goldsmith
authors.forename: Qili
authors.initials: Q
authors.lastname: Feng
authors.forename: Qingyou
authors.initials: Q
authors.lastname: Xia
authors.forename: Kimiko
authors.initials: K
authors.lastname: Yamamoto
authors.forename: Toru
authors.initials: T
authors.lastname: Shimada
authors.forename: Kazuei
authors.initials: K
authors.lastname: Mita
mesh_terms: D000818:Animals; D012831:Bombyx / Q000235:genetics*; D002874:Chromosome Mapping; D018076:DNA, Complementary / Q000235:genetics*; D030541:Databases, Genetic; D005091:Exons; D020224:Expressed Sequence Tags; D005260:Female; D015723:Gene Library; D016678:Genome; D007438:Introns; D008297:Male; D008954:Models, Biological; D008969:Molecular Sequence Data; D005810:Multigene Family; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D018076:DNA, Complementary
keywords: Bombyx mori; gene cluster; large-scale full-length cDNA collection; sexual dimorphism; silkworm; tissue-specific genes